Red Hat's stock may have just had its worst trading day since 2006 after the company's earnings guidance underwhelmed Wall Street, but that won't matter in the longer term, CEO Jim Whitehurst told CNBC on Friday.

While the open-source software company beat analysts' top- and bottom-line estimates, it missed their estimates for the fiscal second-quarter forecast.

One pain point for Red Hat, which helps enterprises connect to the cloud and link various applications together, was its lighter-than-expected billings results.

Whitehurst emphasized that, in the last 10 years, management has repeatedly informed investors about the inherent volatility of Red Hat's billings.

"The last time I was on [Mad Money], ... we had kind of a light billings quarter and the stock dropped a lot then and then, obviously, has doubled since then," the CEO said Friday. "We don't manage the billings because they're not a great indicator of the health of the company and so, because analysts look at billings, that creates some volatility and we just learn to live with that."

Adding that "it's one quarter," Whitehurst told Cramer he expected some of the weakness came from analysts anticipating a "beat-and-raise" quarter rather than one that was in line with Red Hat's guidance.

"We had a really great year last year, which creates tough comps," he admitted. "We said what we would do, we delivered that, we reaffirmed guidance for the year other than pulling down for currency, but I think there was a sense that we were going to really blow it out and, frankly, we just delivered what we said we'd deliver. And that created a bit of disappointment."

Red Hat's longer term deals — and the 65 percent year-over-year growth it had in deals over $1 million — should sustain the company through the stock's downturn, Whitehurst said.